Merge pull request #634 from stan-dev/v0.5.0

CmdStanR v0.5.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: cmdstanr
 Title: R Interface to 'CmdStan'
-Version: 0.4.0.9001
-Date: 2021-04-15
+Version: 0.5.0
+Date: 2022-03-17
 Authors@R: 
     c(person(given = "Jonah", family = "Gabry", role = c("aut", "cre"),
            email = "[email protected]"),

NEWS.md

@@ -1,4 +1,4 @@
-# cmdstanr 0.4.0.9000
+# cmdstanr 0.5.0
 
 ### Bug fixes
 
@@ -19,59 +19,62 @@ will continue to be supported until version 1.0 but `install_cmdstan()` will now
 default to `.cmdstan` and CmdStanR will first look for `.cmdstan` before falling
 back on `.cmdstanr`. (#454)
 
-* Expose CmdStan's `diagnose` method that compares Stan's gradient computations
-to gradients computed via finite differences. (#485)
-
-* `write_stan_file()` now choose file names deterministically based on the code
-so that models do not get unnecessarily recompiled when calling the function
-multiple times with the same code. (#495, @martinmodrak)
+* New method `diagnose()` for CmdstanModel objects exposes CmdStan's `diagnose`
+method for comparing Stan's gradient computations to gradients computed via
+finite differences. (#485)
 
 * New method `$variables()` for CmdstanModel objects that returns a list of
 variables in the Stan model, their types and number of dimensions. Does
 not require the model to be compiled. (#519)
 
-* `write_stan_json()` now handles data of class `"table"`. Tables are converted
-to vector, matrix, or array depending on the dimensions of the table. (#528)
-
-* `install_cmdstan()` now automatically installs the Linux ARM CmdStan when
-Linux distributions running on ARM CPUs are detected. (#531)
-
-* The `dir` argument for `write_stan_file()` can now be set with a global
-option. (#537)
-
-* Improved processing of named lists supplied to the `data` argument to JSON
-data files: checking whether the list includes all required elements/Stan
-variables; improved differentiating arrays/vectors of length 1 and scalars
-when generating JSON data files; generating floating point numbers with
-decimal points to fix issue with parsing large numbers. (#538)
+* New method `$format()` for auto-formatting and canonicalizing the Stan models. (#625)
 
 * Added the option to create `CmdStanModel` from the executable only with the
 `exe_file` argument. (#564)
 
 * Added a convenience argument `user_header` to `$compile()` and `cmdstan_model()`
 that simplifies the use of an external .hpp file to compile with the model.
 
+* Added the `cmdstanr_force_recompile` global option that is used for forcing
+recompilation of Stan models. (#580)
+
 * New method `$code()` for all fitted model objects that returns the Stan code
 associated with the fitted model. (#575)
 
-* Added the `cmdstanr_force_recompile` global option that is used for forcing
-recompilation of Stan models. (#580)
+* New method `$diagnostic_summary()` for CmdStanMCMC objects that summarizes the
+sampler diagnostics (divergences, treedepth, ebfmi) and can regenerate the
+related warning messages. (#205)
+
+* New `diagnostics` argument for the `$sample()` method to specify which
+diagnostics are checked after sampling. Replaces `validate_csv` argument. (#205)
+
+* Added E-BFMI checks that run automatically post sampling. (#500, @jsocolar)
 
 * New methods for `posterior::as_draws()` for CmdStanR fitted model objects.
 These are just wrappers around the `$draws()` method provided for convenience. (#532)
 
-* Added E-BFMI checks that run automatically post sampling. (#500, @jsocolar)
+* `write_stan_file()` now choose file names deterministically based on the code
+so that models do not get unnecessarily recompiled when calling the function
+multiple times with the same code. (#495, @martinmodrak)
 
-* New method `$diagnostic_summary()` that summarizes the sampler diagnostics
-(divergences, treedepth, ebfmi) and can regenerate the related warning messages. (#205)
+* The `dir` argument for `write_stan_file()` can now be set with a global
+option. (#537)
 
-* New `diagnostics` argument for the `$sample()` method to specify which
-diagnostics are checked after sampling. Replaces `validate_csv` argument. (#205)
+* `write_stan_json()` now handles data of class `"table"`. Tables are converted
+to vector, matrix, or array depending on the dimensions of the table. (#528)
+
+* Improved processing of named lists supplied to the `data` argument to JSON
+data files: checking whether the list includes all required elements/Stan
+variables; improved differentiating arrays/vectors of length 1 and scalars
+when generating JSON data files; generating floating point numbers with
+decimal points to fix issue with parsing large numbers. (#538)
+
+* `install_cmdstan()` now automatically installs the Linux ARM CmdStan when
+Linux distributions running on ARM CPUs are detected. (#531)
 
 * New function `as_mcmc.list()` for converting CmdStanMCMC objects to mcmc.list
 objects from the coda package. (#584, @MatsuuraKentaro)
 
-* New method `$format()` for auto-formatting and canonicalizing the Stan models.
 
 # cmdstanr 0.4.0
 

R/model.R

@@ -1,11 +1,10 @@
 #' Create a new CmdStanModel object
 #'
-#' @description \if{html}{\figure{logo.png}{options: width="25px"
-#'   alt="https://mc-stan.org/about/logo/"}} Create a new [`CmdStanModel`]
-#'   object from a file containing a Stan program or from an existing Stan
-#'   executable. The [`CmdStanModel`] object stores the path to a Stan program
-#'   and compiled executable (once created), and provides methods for fitting
-#'   the model using Stan's algorithms.
+#' @description \if{html}{\figure{logo.png}{options: width="25"}}
+#'   Create a new [`CmdStanModel`] object from a file containing a Stan program
+#'   or from an existing Stan executable. The [`CmdStanModel`] object stores the
+#'   path to a Stan program and compiled executable (once created), and provides
+#'   methods for fitting the model using Stan's algorithms.
 #'
 #'   See the `compile` and `...` arguments for control over whether and how
 #'   compilation happens.
@@ -444,7 +443,7 @@ compile <- function(quiet = TRUE,
   if (is.null(include_paths) && !is.null(private$precompile_include_paths_)) {
     include_paths <- private$precompile_include_paths_
   }
-  private$include_paths_ <- include_paths  
+  private$include_paths_ <- include_paths
   if (is.null(dir) && !is.null(private$dir_)) {
     dir <- absolute_path(private$dir_)
   } else if (!is.null(dir)) {
@@ -772,7 +771,7 @@ check_syntax <- function(pedantic = FALSE,
 }
 CmdStanModel$set("public", name = "check_syntax", value = check_syntax)
 
-#' Run stanc's auto-formatter on the model code. 
+#' Run stanc's auto-formatter on the model code.
 #'
 #' @name model-method-format
 #' @aliases format
@@ -815,7 +814,7 @@ CmdStanModel$set("public", name = "check_syntax", value = check_syntax)
 #'   real                     lambda;
 #' }
 #' model {
-#'   target += 
+#'   target +=
 #'  poisson_log(y | lambda);
 #' }
 #' ")
@@ -851,7 +850,7 @@ format <- function(overwrite_file = FALSE,
     max_line_length,
     lower = 1, len = 1, null.ok = TRUE
   )
-  stanc_options <- private$precompile_stanc_options_  
+  stanc_options <- private$precompile_stanc_options_
   stancflags_val <- include_paths_stanc3_args(private$precompile_include_paths_)
   stanc_options["auto-format"] <- TRUE
   if (!is.null(max_line_length)) {
@@ -915,7 +914,7 @@ format <- function(overwrite_file = FALSE,
     out_file <- self$stan_file()
   }
   cat(run_log$stdout, file = out_file, sep = "\n")
-  
+
   invisible(TRUE)
 }
 CmdStanModel$set("public", name = "format", value = format)

_pkgdown.yml

@@ -101,6 +101,7 @@ reference:
       - CmdStanMLE
       - CmdStanVB
       - CmdStanGQ
+      - CmdStanDiagnose
       - starts_with("fit-method")
   - title: "Other tools for working with CmdStan"
     contents: